Mucoepidermoid carcinoma is a mixed cell tumor with both adenocarcinomatous and squamous components. We report a rare case of superficial mucoepidermoid carcinoma of the esophagus with mucosal gastric cancer. Endoscopic mucosal resection was performed on a 67-year-old man with a slight but defined depressed lesion of the thoracic esophagus and two lesions of mucosal gastric cancer. Histological examination revealed that the lesion of the esophagus was a mucoepidermoid carcinoma and the two lesions of the stomach were well-differentiated adenocarcinoma. Since the mucoepidermoid carcinoma had only slightly invaded the submucosal layer, it was thought to arise from the ductal epithelium of the esophageal gland or the stratified squamous epithelium of the esophagus. Radiation therapy with a total dose of 60 Gy was performed and there has been no recurrence or metastasis to other organs during 36 months of follow-up.